I'm having working on modeling a sulfur on the phosphate backbone of DNA in replace of one of the oxygens and have encountered some restraint problems. I've successfully managed to replace the oxygen with a sulfur in the proper geometry in a pdb, generate a cif file for the modified residue (adenosine 5'-phosphorothioate), and run an initial refinement. Upon that refinement, a few errors occur. First, since the phosphate bound to the sulfur is the first atom of the modified residue the angle between the O3' (of the neighboring residue) - P- S is not recognized and forced into an unfavorable geometry. When trying to add that additional angle to the cif file, I get an error. Aditionally, the change causes Phenix to not recognize the chirality of the C3' that the phosphate is bonded to and forces the ribose into a planar conformation. I am sure there is something I am missing that allows phenix to recognize this new residue as a modified nucleotide so that it knows these restraints. Any insight on this would be great. Thank you!
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